The goal of this proposal is to employ embryonic stem (ES) cell and induced pluripotent stem (iPS) cell systems to define the genetic and epigenetic programs of the earliest stages of human development, and to decipher whether identifiable components of these programs differ in iPS cells derived from individuals with the two most common inherited lung diseases: cystic fibrosis (CF) or alpha-1 antitrypsin (AAT)-related emphysema. For this proposal, we have developed a novel excisable reprogramming vector able to generate 'clinical grade'iPS cells free of any residual reprogramming transgenes, and we have employed this vector to derive the first known lung disease-specific iPS cells from an individual with cystic fibrosis. We propose here to derive additional clinical grade iPS cell lines from individuals with CF and AAT-deficiency, in order to test the hypothesis that these cells are able to express the complete genetic developmental programs of early human germ layer specification, but deviate from normalcy only upon differentiation into epithelial lineages known to express the inherited mutations. First, we will define the genetic and epigenetic programs of differentiating endodermal cell lineages at defined stages of early human development, using ES and iPS cell model systems. Next we proposed, to determine whether the genetic programs of these differentiated lineages differ when derived from iPS cells of CF or AAT mutant genotypes in comparison to those derived from normal iPS or ES cells. PUBLIC HEALTH RELEVANCE: Cystic fibrosis and alpha-1 antitrypsin deficiency-related emphysema are the two most common inherited lung diseases. This proposal develops induced pluripotent stem cells from skin biopsies of normal controls as well as individuals with these diseases. These stem cells will be utilized to better understand the genetic programs of cells carrying the mutations responsible for CF and AAT-deficiency and will be employed to develop new in vitro models that will increase an understanding of the biology of these diseases.